Merge poissonconsulting/dev: refactors, bug fixes, dependency and test cleanup

.Rbuildignore

@@ -25,3 +25,4 @@
 .devcontainer
 ^\.vscode$
 ^[.]?air[.]toml$
+^\.claude$

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @joethorley

.github/workflows/test-coverage.yaml

@@ -38,7 +38,7 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v5
+      - uses: codecov/codecov-action@v7
         with:
           # Fail if error if not on PR, or if on PR and token is given
           fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}

DESCRIPTION

@@ -49,8 +49,8 @@ BugReports: https://github.com/bcgov/ssdtools/issues
 Depends:
     R (>= 4.1)
 Imports:
-    abind,
     chk,
+    dplyr,
     furrr,
     generics,
     ggplot2,
@@ -61,7 +61,6 @@ Imports:
     grid,
     lifecycle,
     parallel,
-    plyr,
     purrr,
     Rcpp,
     readr,
@@ -73,37 +72,34 @@ Imports:
     tibble,
     TMB,
     universals,
-    utils
+    utils,
+    VGAM
 Suggests:
     actuar,
     covr,
-    dplyr,
     EnvStats,
     extraDistr,
     fitdistrplus,
     grDevices,
     knitr,
     latex2exp,
-    magrittr,
-    mle.tools,
     patchwork,
-    reshape2,
     rmarkdown,
     testthat (>= 3.0.0),
     tidyr,
-    tidyselect,
     tinytex,
-    VGAM,
     withr
 LinkingTo: 
     Rcpp,
     RcppEigen,
     TMB
-VignetteBuilder: 
+VignetteBuilder:
     knitr
+Remotes:
+    open-AIMS/ssddata
+Config/roxygen2/version: 8.0.0.9000
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3.9000

NAMESPACE

@@ -166,63 +166,91 @@ import(chk)
 import(ggplot2)
 import(rlang)
 importFrom(Rcpp,sourceCpp)
-importFrom(TMB,MakeADFun)
-importFrom(TMB,sdreport)
-importFrom(abind,abind)
-importFrom(furrr,furrr_options)
-importFrom(furrr,future_map)
-importFrom(generics,augment)
-importFrom(generics,glance)
-importFrom(generics,tidy)
-importFrom(ggplot2,autoplot)
-importFrom(ggplot2,sym)
-importFrom(ggplot2,waiver)
+importFrom(TMB,
+  MakeADFun,
+  sdreport
+)
+importFrom(furrr,
+  furrr_options,
+  future_map
+)
+importFrom(generics,
+  augment,
+  glance,
+  tidy
+)
+importFrom(ggplot2,
+  autoplot,
+  sym,
+  waiver
+)
 importFrom(glue,glue)
-importFrom(goftest,ad.test)
-importFrom(goftest,cvm.test)
-importFrom(graphics,par)
-importFrom(graphics,plot)
-importFrom(graphics,title)
-importFrom(grid,gList)
-importFrom(grid,gTree)
-importFrom(grid,gpar)
-importFrom(grid,grobName)
-importFrom(grid,polygonGrob)
-importFrom(grid,segmentsGrob)
-importFrom(lifecycle,deprecate_soft)
-importFrom(lifecycle,deprecate_stop)
-importFrom(lifecycle,deprecate_warn)
-importFrom(lifecycle,deprecated)
-importFrom(lifecycle,expect_defunct)
-importFrom(lifecycle,expect_deprecated)
-importFrom(parallel,nextRNGStream)
-importFrom(parallel,nextRNGSubStream)
-importFrom(plyr,summarise)
-importFrom(purrr,list_assign)
-importFrom(purrr,transpose)
-importFrom(scales,label_percent)
-importFrom(scales,manual_pal)
-importFrom(scales,trans_breaks)
+importFrom(goftest,
+  ad.test,
+  cvm.test
+)
+importFrom(graphics,
+  par,
+  plot,
+  title
+)
+importFrom(grid,
+  gList,
+  gTree,
+  gpar,
+  grobName,
+  polygonGrob,
+  segmentsGrob
+)
+importFrom(lifecycle,
+  deprecate_soft,
+  deprecate_stop,
+  deprecate_warn,
+  deprecated,
+  expect_defunct,
+  expect_deprecated
+)
+importFrom(parallel,
+  nextRNGStream,
+  nextRNGSubStream
+)
+importFrom(purrr,
+  list_assign,
+  transpose
+)
+importFrom(scales,
+  label_percent,
+  manual_pal,
+  trans_breaks
+)
 importFrom(ssddata,gm_mean)
-importFrom(stats,coef)
-importFrom(stats,complete.cases)
-importFrom(stats,ks.test)
-importFrom(stats,logLik)
-importFrom(stats,nobs)
-importFrom(stats,optim)
-importFrom(stats,plogis)
-importFrom(stats,predict)
-importFrom(stats,qlogis)
-importFrom(stats,runif)
-importFrom(stats,sd)
-importFrom(stats,setNames)
-importFrom(stats,uniroot)
-importFrom(stats,weighted.mean)
+importFrom(stats,
+  coef,
+  complete.cases,
+  ks.test,
+  logLik,
+  nobs,
+  optim,
+  plogis,
+  predict,
+  qlogis,
+  runif,
+  sd,
+  setNames,
+  uniroot,
+  weighted.mean
+)
 importFrom(stringr,str_order)
-importFrom(tibble,as_tibble)
-importFrom(tibble,tibble)
-importFrom(universals,estimates)
-importFrom(universals,npars)
-importFrom(utils,capture.output)
-importFrom(utils,relist)
+importFrom(tibble,
+  as_tibble,
+  tibble
+)
+importFrom(universals,
+  estimates,
+  npars
+)
+importFrom(utils,
+  capture.output,
+  relist
+)
 useDynLib(ssdtools, .registration=TRUE); useDynLib(ssdtools_TMBExports)

R/boot.R

@@ -30,12 +30,7 @@ sample_nonparametric <- function(data) {
   data[sample(nrow(data), replace = TRUE), ]
 }
 
-sample_parametric <- function(
-  dist,
-  args = args,
-  weighted = weighted,
-  censoring = censoring
-) {
+sample_parametric <- function(dist, args, weighted, censoring) {
   what <- paste0("ssd_r", dist)
   args$chk <- FALSE
   sample <- do.call(what, args)

R/burrrIII3.R

@@ -98,7 +98,7 @@ sburrIII3 <- function(data, pars = NULL) {
   list(log_scale = 0, log_shape1 = 0, log_shape2 = 0)
 }
 
-bburrIII3 <- function(x, range_shape1, range_shape2, ...) {
+bburrIII3 <- function(range_shape1, range_shape2, ...) {
   log_range_shape1 <- log(range_shape1)
   log_range_shape2 <- log(range_shape2)
   list(

R/devtools-helpers.R

@@ -20,7 +20,6 @@ release_questions <- function() {
     "Have you fixed all the `FIXME`s?",
     "Have you run `data-raw/data-raw.R`?",
     "Have you tested using `ssdtests` package?",
-    "Have you run `vignettestatic/small-sample-bias.Rmd`?",
     "Have you confirmed all images in .Rmd files have alternative text defined using the `fig.alt` argument?",
     "Have you confirmed updated Apache 2.0 license at the top of all code files?",
     "Have you confirmed update Creative Commons license for all non-code files?"

R/estimates.R

@@ -60,6 +60,8 @@ estimates.fitdists <- function(x, all_estimates = FALSE, ...) {
 }
 
 .relist_estimates <- function(x) {
-  list <- relist(x, skeleton = emulti_ssd())
+  skeleton <- emulti_ssd()
+  x <- unlist(x)[names(unlist(skeleton))]
+  list <- relist(x, skeleton = skeleton)
   purrr::map(list, function(x) as.list(unlist(x)))
 }

R/ggproto.R

@@ -27,7 +27,7 @@ StatSsdpoint <- ggproto(
   "StatSsdpoint",
   Stat,
   required_aes = "x",
-  default_aes = aes(y = ..density..),
+  default_aes = aes(y = after_stat(density)),
   compute_panel = function(data, scales) {
     data$density <- ssd_ecd(data$x)
     data
@@ -40,7 +40,7 @@ StatSsdsegment <- ggproto(
   "StatSsdsegment",
   Stat,
   required_aes = c("x", "xend"),
-  default_aes = aes(y = ..density.., yend = ..density..),
+  default_aes = aes(y = after_stat(density), yend = after_stat(density)),
   compute_panel = function(data, scales) {
     data$density <- ssd_ecd(rowMeans(data[c("x", "xend")], na.rm = TRUE))
     data
@@ -114,18 +114,17 @@ GeomXribbon <- ggproto(
     # Check that aesthetics are constant
     aes <- unique(data[c("colour", "fill", "linewidth", "linetype", "alpha")])
     if (nrow(aes) > 1) {
-      err("Aesthetics can not vary with a ribbon.")
+      err("Aesthetics cannot vary with a ribbon.")
     }
     aes <- as.list(aes)
 
     missing_pos <- !complete.cases(data[c("y", "xmin", "xmax")])
     ids <- cumsum(missing_pos) + 1
     ids[missing_pos] <- NA
 
-    positions <- plyr::summarise(
-      data,
-      y = c(y, rev(y)),
-      x = c(xmax, rev(xmin)),
+    positions <- data.frame(
+      y = c(data$y, rev(data$y)),
+      x = c(data$xmax, rev(data$xmin)),
       id = c(ids, rev(ids))
     )
     munched <- coord_munch(coord, positions, panel_params)

R/gompertz.R

@@ -141,7 +141,6 @@ rgompertz <- function(n, llocation = 0, lshape = 0) {
 }
 
 sgompertz <- function(data, pars = NULL) {
-  rlang::check_installed("VGAM")
   x <- mean_weighted_values(data)
 
   if (!is.null(pars)) {